FLOCK & TRACE 3.1

FLOCK is designed to unravel genetic structure within a collection of genotypes, whether pure or admixed. It is assumed that pure, “source”, samples are not available. The program may be used to solve the “number (K) of populations” problem. Since FLOCK is a non-model algorithm, the populations may originate from sexual as well as clonal reproduction. When K is already known, it may be used to separate pure and admixed specimens into K groups.  FLOCK is a non- Bayesian, non MCMC, method and therefore differs substantially from previous clustering algorithms and processing time is much shorter (20 sweeps). Its working principle is repeated re-allocation of all collected specimens (total sample) to k subsamples.

The methods to map genetic admixture on a set of samples (K known) and to estimate the number of populations K were described respectively in: 

Duchesne P, Turgeon J (2009) FLOCK: a method for quick mapping of admixture without source samples. Molecular Ecology Resources 9: 1333-1344

Duchesne P, Turgeon J (2012) FLOCK Provides Reliable Solutions to the "Number of Populations" Problem Journal of Heredity 2012; doi: 10.1093/jhered/ess038

Three versions of FLOCK are available, one for microsatellite, one for AFLP and one for SNP markers. The basic algorithm, input and output formats are the same in the three versions.